5C8U

Crystal structure of the SARS coronavirus nsp14-nsp10 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex

Ma, Y.Y.Wu, L.J.Shaw, N.Gao, Y.Wang, J.Sun, Y.N.Lou, Z.Y.Yan, L.M.Zhang, R.G.Rao, Z.H.

(2015) Proc Natl Acad Sci U S A 112: 9436-9441

  • DOI: 10.1073/pnas.1508686112
  • Primary Citation of Related Structures:  
    5C8S, 5C8U, 5C8T

  • PubMed Abstract: 
  • Nonstructural protein 14 (nsp14) of coronaviruses (CoV) is important for viral replication and transcription. The N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as a (guanine-N7) methyl transferase (N7-MTase) for mRNA capping ...

    Nonstructural protein 14 (nsp14) of coronaviruses (CoV) is important for viral replication and transcription. The N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as a (guanine-N7) methyl transferase (N7-MTase) for mRNA capping. The molecular basis of both these functions is unknown. Here, we describe crystal structures of severe acute respiratory syndrome (SARS)-CoV nsp14 in complex with its activator nonstructural protein10 (nsp10) and functional ligands. One molecule of nsp10 interacts with ExoN of nsp14 to stabilize it and stimulate its activity. Although the catalytic core of nsp14 ExoN is reminiscent of proofreading exonucleases, the presence of two zinc fingers sets it apart from homologs. Mutagenesis studies indicate that both these zinc fingers are essential for the function of nsp14. We show that a DEEDh (the five catalytic amino acids) motif drives nucleotide excision. The N7-MTase domain exhibits a noncanonical MTase fold with a rare β-sheet insertion and a peripheral zinc finger. The cap-precursor guanosine-P3-adenosine-5',5'-triphosphate and S-adenosyl methionine bind in proximity in a highly constricted pocket between two β-sheets to accomplish methyl transfer. Our studies provide the first glimpses, to our knowledge, into the architecture of the nsp14-nsp10 complex involved in RNA viral proofreading.


    Organizational Affiliation

    Laboratory of Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; National Center for Protein Science Shanghai, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, Chengdu, Sichuan 610041, China; Collaborative Innovation Center for Biotherapy Chengdu, Sichuan 610041, China raozh@mail.tsinghua.edu.cn rzhang@sun5.ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 10A, C144Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine-N7 methyltransferaseB, D528Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
EC: 2.1.1 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.928α = 90
b = 194.979β = 90
c = 179.844γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of China Project 973China2014CB542800
Ministry of Science and Technology of China Project 973China2014CBA02003
National Natural Science Foundation of ChinaChina81330036
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08020200

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references